+ public boolean setHiddenColumns(HiddenColumns cols)
+ {
+ boolean changed = cols == null ? hiddenCols != null
+ : !cols.equals(hiddenCols);
+ hiddenCols = cols;
+ return changed;
+ }
+
+ @Override
+ public void setupJPredAlignment()
+ {
+ SequenceI repseq = getSequenceAt(0);
+ setSeqrep(repseq);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideList(repseq.getInsertions());
+ setHiddenColumns(cs);
+ }
+
+ @Override
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ return propagateInsertions(profileseq, origseq, nview);
+ }
+
+ /**
+ *
+ * @param profileseq
+ * sequence in al which corresponds to origseq
+ * @param al
+ * alignment which is to have gaps inserted into it
+ * @param origseq
+ * sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ private HiddenColumns propagateInsertions(SequenceI profileseq,
+ SequenceI origseq, HiddenColumns hc)